A new synthesis by two Santa Fe Institute researchers offers a coherent picture of how metabolism, and thus all life, arose. The study, published December 12, 2012, in the journal Physical Biology, offers new insights into how the complex chemistry of metabolism cobbled itself together, the likelihood of life emerging and evolving as it did on Earth, and the chances of finding life elsewhere. Click on the image or the title to see the Sante Fe article or go to http://iopscience.iop.org/1478-3975/10/1/011001/article to see the paper which is worth a read.

A potent theory has emerged explaining a mysterious statistical law that arises throughout physics and mathematics.

ComplexInsight's insight:

Systems of many interacting components — be they species, integers or subatomic particles — kept producing the same statistical curve, which had become known as the Tracy-Widom distribution. This puzzling curve seemed to be the complex cousin of the familiar bell curve, or Gaussian distribution, which represents the natural variation of independent random variables like the heights of students in a classroom or their test scores... click on title to read more.

Knowing which machine learning method to apply for a given problem takes time to learn - fortunately the fine folks over at scikit-learn.org have created a quick visual cheatsheet that helps understand which algorithm to apply in which context. Very helpful.

Interesting article on the work of Yoshiki Sasai a Japanese biologist and Director of the Laboratory for Organogenesis and Neurogenesis at the research institute RIKEN in Kobe, Japan. Sasai was best known for developing new methods to grow stem cells into organ-like structures

This 2009 publication from the FAO’s Forestry and Forest Products Division highlights why emerging infectious diseases are considered to be among today’s major challenges to science, global health and human development. Rapid changes associated with globalization, especially the rapidly increasing ease of transport, are mixing people, domestic animals, wildlife and plants, along with their parasites and pathogens, at a frequency and in combinations that are unprecedented.

ComplexInsight's insight:

This prescient report from the FAO in 2009 highlights why research on EIDs, particularly that involving the ecological epidemiology of zoonotic and vector-borne diseases associated with forests, needs to be integrated with forest resource management and planning and healthcare management planning. This report along with related publications from FAO are essential reading for anyone modeling ecological change and disease impact. Very much worth reading.

As humans transform ecosystems and come into closer contact with animals, scientists fear more viral epidemics

ComplexInsight's insight:

After publishing the link to the paper on ebola antibodies in fruitbats in Bangladesh - wespeculated and were asked regarding deforestation impact - this is a good overview article discussing some of the current discussion points.

Our bodies are a genetic patchwork, possessing variation from cell to cell. Is that a good thing?

ComplexInsight's insight:

With new methods of single cell DNA sequencing becoming available - biologists are beginning to look a the degrees of variations that exist across cells and the extent of cell to cell diversity and what this implies for biological adaptation.

Say what you will about Oracle co-founder and CEO Larry Ellison, but when the software giant bought Sun Microsystems more than four years ago, for $7.4 bil

ComplexInsight's insight:

It has often been easy to forget following the acquisition of Sun by Oracle - Oracle have continued investing in hardware. The new M7 chip line with 64 sparc cores and Numa interconnect options not only continues to promise speed increases for existing oracle customers but also shows benefits over off the shelf clusters of highly integrated large core systems using optimised connection architectures. Good in depth article - worth reading.

Food Safety News How CDC Uses Antibiotic Resistance Data Food Safety News Over the past year, you may have noticed that antimicrobial resistance information has been incorporated in the outbreak reports put out by the Centers for Disease Control...

ComplexInsight's insight:

CDC are one fo the organisations leading information release on antimicrobial resistance. This article explaines where to find out more info from CDC on this area. Worth reading.

"Silicon is so passé. Those who are truly au courant in the coding world are working with carbon—specifically DNA, that most ancient and elegant of codes. Such biohacking is central to the rapidly expanding field of synthetic biology, a term that somehow seems a little threatening to many of us who are the products of the old fashioned kind of biology that’s been around since the planet first managed to gin up a few primitive prokaryotes 3.5 billion years ago.

That’s especially because messing around with DNA is increasingly a garage band kind of venture. The basic techniques and technology are now sufficiently disseminated so that any reasonably bright and inquisitive person can do all kinds of interesting things in a home or community lab. And—gulp—might that not include weaponizing Ebola or involve some other highly anti-social endeavor?

Relax (really). Those fears are overblown, opines Nina DiPrimio, the editor of BioCoder, a quarterly published by and for the DIYbio (as in, Do It Yourself biology) community.

In the first place, says DiPrimio, endowing viruses with new and ever-more-lethal characteristics requires the kind of equipment and skill sets usually found only in large government or corporate labs. Second, if anyone wants to attempt it, the mischief-maker wouldn’t need to figure out how to manipulate Ebola or HIV. Relatively simple procedures already are known for weaponizing basic old anthrax, or manufacturing and distributing astoundingly powerful poisons such as ricin, or—well, you get the idea.

“It takes a lot of skill and equipment to do bad things” with gene-spliced microbes says DiPrimio, until recently a postdoctoral researcher at UC Berkeley and the co-organizer of the university’s Synthetic Biology Super Group. “A DNA cloning class won’t teach you how to create something pathogenic. That isn’t to say potential dangers should be ignored. At a certain point, regulation (of homegrown biohacking) is likely. We don’t know what that will look like, but the community is aware of it and discussing it.”

DiPrimio is also deeply concerned about safety within these do-it-yourself operations. BioCoder’s articles include pointers to ensure one’s lab is legal, and emphasize basic protocols so tyro researchers don’t burn, blow up or electrocute themselves. But first and foremost, the publication serves as an agora for the biohacking community...."

cientists have made an amplifier to boost biological signals, using DNA and harmless E. coli bacteria.

Conventional amplifiers, such as those that are combined with loudspeakers to boost the volume of electric guitars and other instruments, are used to increase the amplitude of electrical signals. Now scientists from Imperial College London have used the same engineering principles to create a biological amplifier, by re-coding the DNA in the harmless gut bacteria Escherichia coli bacteria (E. coli).
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"Scientists have made an amplifier to boost biological signals, using DNA and harmless E. coli bacteria.

Conventional amplifiers, such as those that are combined with loudspeakers to boost the volume of electric guitars and other instruments, are used to increase the amplitude of electrical signals.

Now scientists from Imperial College London have used the same engineering principles to create a biological amplifier, by re-coding the DNA in the harmless gut bacteria Escherichia coli bacteria (E. coli).

The team say this ‘bio-amplifier’ might be used in microscopic cellular sensors , which scientists have already developed, that could detect minute traces of chemicals and toxins, to make them more sensitive. Ultimately, this could lead to new types of sensors to detect harmful toxins or diseases in our bodies and in the environment before they do any damage.

In laboratory tests, the team’s bio-amplifier was able to significantly boost the detection limit and sensitivity of a sensor designed to detect the toxin arsenic. The device is also modular, which means that the devices can be easily introduced in different genetic networks, and can potentially be used to increase the sensitivity and accuracy of a broad range of other genetic sensors to detect pathogens and toxins.

The results of the study are published in the journal Nucleic Acids Research.

Dr Baojun Wang, who is now based at the University of Edinburgh, but carried out the study while in the Division of Cell and Molecular Biology at Imperial, said: “One potential use of this technology would be to deploy microscopic sensors equipped with our bio-amplifier component into a water network. Swarms of the sensors could then detect harmful or dangerous toxins that might be hazardous to our health. The bio-amplifiers in the sensors enable us to detect even minute amounts of dangerous toxins, which would be of huge benefit to water quality controllers.”

Scientists have previously known that cells have their own inbuilt amplifiers to first detect and then boost biological signals, which are crucial for survival and reproduction. They have been attempting to understand how they work in more detail so as to remodel them for other applications. However the challenge for scientists has been engineering a device that can predictably amplify signals without distortion or feedback.

In the study, scientists first re-engineered genes involved in a special cell network called hrp (hypersensitive response and pathogenicity), which have naturally occurring amplifying proteins that function just like an electronic amplifier. They then cloned these amplifying components and inserted them into the harmless gut bacteria E. coli, fitting it with a synthetic arsenic input sensor and a fluorescent green protein gene as the output. ..."

Bio-IT World Transcriptic Aims to Make the Biology Lab Programmable Bio-IT World At a time when monkeys are exerting telepathic control over mechanical limbs, most biologists still don't have access to robotics for even the simplest procedures.

ComplexInsight's insight:

Transcriptic is an awesomely promising start up - that aims to provide automated execution of different lab protocols. Intersting article at Bio-IT World. If you are interested in the future of weblab work and how it connects to synthetic biology and bio discovery - well worth reading.

Following the WHO decision that it was ethical to use untested drugs on Ebola patients if it gave them a possibility of recovery, Canada says it will donate up to 1,000 doses of an experimental Ebola vaccine to help battle the disease's outbreak in West Africa.

The meat-eating theropod dinosaurs shrank 12 times in a row, going from over 200 kilograms to less than a kilogram, until they were small enough to fly

ComplexInsight's insight:

Evidence in a study by Mike Lee of the South Australian Museum in Adelaide and colleagues has shown that a gradual wave of evolution led theropods to evolve into modern birds. Great article from New Scientist on Mike Lee's research work.

Awesome article on the Maximum Entropy (MaxEnt) theory proposed by John Harte, professor of ecology at University of California, Berkeley. MaxEnt is a key tool to help calculate the total number of species in ecosystem based on very limited information.

Where do a zebra’s stripes, a leopard’s spots and our fingers come from? The key was found years ago – by the man who cracked the Enigma code, writes Kat Arney.

ComplexInsight's insight:

Alan Turing’s published his ‘chemical morphogenesis’ research paper in 1952, 2 years before his tragic and untimely death. The paper opened the discussion on how computation and biology may be at fundamentally linked, a thread which continues to be ripe with exploration today. Great article from Mosaic Science explaining the ideas in turings paper and the 60 years of subsequent research.

The annual estimates reflect amounts that change as a result of science, actual research projects funded, and the NIH budget. The research categories are not mutually exclusive. Individual research projects can be included in multiple categories so amounts depicted within each column of this table do not add up to 100 percent of NIH-funded research. The table shows historical data for FY 2010 through FY 2013. The FY 2014-2015 estimates are based on RCDC actual data.

ComplexInsight's insight:

Table of US research expenditure estimates by NIH for various research, health conditions and disease categories.

The precise factors that result in an Ebola virus outbreak remain unknown, but a broad examination of the complex and interwoven ecology and socioeconomics may help us better understand what has already happened and be on the lookout for what might happen next, including determining regions and populations at risk. Although the focus is often on the rapidity and efficacy of the short-term international response, attention to these admittedly challenging underlying factors will be required for long-term prevention and control.

ComplexInsight's insight:

As terrifying and tragic the current Ebola outbreak is - informed discussion on sources, vectors and the interplay of ecology and socioeconomics will be at the heart of finding long term solutions.

To determine geographic range for Ebola virus, we tested 276 bats in Bangladesh. Five (3.5%) bats were positive for antibodies against Ebola Zaire and Reston viruses; no virus was detected by PCR. These bats might be a reservoir for Ebola or Ebola-like viruses, and extend the range of filoviruses to mainland Asia.

ComplexInsight's insight:

As evidence builds that fruit bats may be a vector for the recent ebola outbreak in Western Africa - I was reminded of this paper in CDC's EID journal which found 5 out of 276 (3.5%) tested bats in Bangladesh had antibodies to Ebola. It would be interesting to map ebola outbreaks against natural migration and deforestation paths and see if there is any correlation and to see how other regional antibody presence tests indicate migration as well. The original paper and the EID journal in general are well worth reading. Click image or headling to read more.

The NVIDIA® CUDA® Toolkit provides a comprehensive development environment for C and C++ developers building GPU-accelerated applications. The CUDA Toolkit includes a compiler for NVIDIA GPUs, math libraries, and tools for debugging and optimizing the performance of your applications.

ComplexInsight's insight:

New CUDA 6 toolkit release with 64-bit arm support, improved CUDA Fortran for scientific aplications, replay features in visual profiler and nvprof and a new BLAS GPU library cublasXT that scales across GPUs. A lot of goodness for compute developers - available here: https://developer.nvidia.com/cuda-downloads

A couple months back, Mark Buchannan wrote an article in which he argued that ABMs might be a productive way of trying to understand the economy. In fact, he went a bit further – he said that ABMs...

ComplexInsight's insight:

Been a while since we published anything on economics but with over 20 years experience building agent based models - we are suckers for articles that encourage people to discover them as thinking tools. Good explanation on how agent based models fit into economic forecasting.

At Radcliffe Institute of Advanced Study at Harvard, Roy Bar-Ziv is expanding his research to explore the paradigm of programmable on-chip DNA compartments as artificial cells, in which the essential reactions of living cells encoded in DNA take place inside miniaturized compartments fabricated in silicon. Understanding the emergent properties of these compartments may lead to assembly of artificial cells capable of computation, autonomous sensing, and replication, with applications in future technologies.

"The assembly of artificial cells capable of executing synthetic DNA programs has been an important goal for basic research and biotechnology. We assembled two-dimensional DNA compartments fabricated in silicon as artificial cells capable of metabolism, programmable protein synthesis, and communication. Metabolism is maintained by continuous diffusion of nutrients and products through a thin capillary, connecting protein synthesis in the DNA compartment with the environment. We programmed protein expression cycles, autoregulated protein levels, and a signaling expression gradient, equivalent to a morphogen, in an array of interconnected compartments at the scale of an embryo. Gene expression in the DNA compartment reveals a rich, dynamic system that is controlled by geometry, offering a means for studying biological networks outside a living cell."

An indispensable part of our personal and working lives, computing has also become essential to industries and governments. Steady improvements in computer hardware have been supported by periodic doubling of transistor densities in integrated circuits over the past fifty years. Such Moore scaling now requires ever-increasing efforts, stimulating research in alternative hardware and stirring controversy. To help evaluate emerging technologies and increase our understanding of integrated-circuit scaling, here I review fundamental limits to computation in the areas of manufacturing, energy, physical space, design and verification effort, and algorithms. To outline what is achievable in principle and in practice, I recapitulate how some limits were circumvented, and compare loose and tight limits. Engineering difficulties encountered by emerging technologies may indicate yet unknown limits.

Discussion of limits is key to creating new ideas - Igor Markov's paper is worth reading for exploring lmitations and engineering implications and to trigger off new discussions and ideas. Worth reading.

E&T magazine Internet of Things Gains Real World Traction Automation World More than many other such pronouncements, this statement, made by Jim Robinson of Intel's Internet of Things Group, during a panel discussion at National Instruments' NI...

ComplexInsight's insight:

While IoT is going through its peak on the hype cycle - stories such as this from Airbus regarding instrumenting the entire production process highlight many of the possibilities. As with any long term technology change, IoT is better described and extrapolated from the small deploymnent stories that indicate its real future. as opposed to the analyst and booster hype.

They don't have a three-second memory. And one researcher thinks we've been dramatically underestimating their intelligence all along.

ComplexInsight's insight:

Culum Brown's research into fish behaviour is deeply revealing both for the insights into aquatic life and into human prejudice regarding other species capabilities. Good article on vox.com regarding fish sentience, perception and behavioural evolution - worth reading.

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